I think that your good common sense is on target here. His laughter and snickers and covering his face when you discuss this uncomfortable subject are a nervous response--his way of showing his anxiety over having to "face the music" about something he knows he is in trouble for.
Given his good reports from his pre-K teachers and your knowing your boy is a good kid, I would chalk up this little "blip on the screen" to early school jitters. You rightly need to be concerned about his chucking rocks at kids if he becomes frustrated or angry with them. So be patient with him and remind him of all the good things he does daily and of all the new things he's accomplishing in school. Teach him to use his words when he disagrees with a child or adult and role-play the different ways he can respond in non-physical ways.